The focus of biology education has shifted from memorization to conceptual understanding of core biological concepts such as matter and energy relationships. To examine undergraduate learning about matter and energy, we incorporated constructed-response (CR) questions into an interactive computer-based tutorial. The objective of this tutorial is to teach students about matter and energy and help dispel common misconceptions through the context of cellular respiration. We used a constructed-response classifier (CRC) tool to categorize ideas in responses to three CR questions and measure changes in student thinking about cellular respiration. Our data set includes 841 undergraduates from 19 geographically diverse institutions including two-year colleges, primarily undergraduate institutions, and research-intensive colleges and universities. We found students from all institution types included more scientific ideas in CRs post-tutorial. Students used an average of 2.1 ideas in CRs and frequently used both scientific and developing ideas. We found this mixed thinking persisted after the tutorial regardless of institution type. Students' multiple-choice (MC) selections were correlated with their CRs, but CRs revealed more mixed thinking than would be inferred from MC responses. Our study shows a CRC tool can measure student learning after a computer-based tutorial and provides more complete information than MC responses.